20.109(S16): System engineering report

Link back to Module 2.

Overview

The culminating assignment for Module 2 will be a research article in which you describe your system engineering investigation. While your Module 1 assignments contained many of the same elements that you'll include here, the research article will be a more complete, cohesive, and formal document. The term research article (as opposed to laboratory report) is meant to indicate your growing maturity as scientific writers, and our growing expectations of you. While your Module 1 assignments contained many of the same elements that you'll include here, the research article will be a more complete, cohesive, and formal document. Your Module 2 research article should approach the quality of the primary scientific literature (excepting its lack of experiment repetition), especially with respect to explaining rather than merely documenting your observations.

The target audience for this report is a scientifically literate reader who is unfamiliar with your specific field. Thus, you can assume rapid comprehension – but not a priori knowledge – of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.

Writing a "research article" versus a "lab report"

A quick but unscientific survey of several journal's "instructions for authors" shows some common themes that are worth considering here. For instance, the instructions from JCB say:

"To warrant publication in the JCB, a manuscript must provide novel and significant mechanistic insight into a cellular function that will be of interest to a general readership. Manuscripts containing purely descriptive observations will not be published."

Similarly, the instructions from MCBstate:

"MCB is devoted to the advancement and dissemination of fundamental knowledge concerning the molecular biology of eukaryotic cells, of both microbial and higher organisms. In most cases, reports that emphasize methods and nucleotide sequence data alone (without experimental documentation of the functional significance of the sequence) will not be considered."

Clearly the goal of published research is not merely to catalog or describe observations but to collect the information into some coherent story that advances general understanding and provides insights that others can use. This is the critical difference between a "lab report" which primarily describes your observations and the "research article" you'll write which invites you to share the insights your data gives. Here you must frame your results to address a larger question that's of general interest to the community. Many of the format instructions that applied to a lab report also apply to your research article, but keep in mind how the intention of the two written assignments differs.

Be sure to review the 20.109 statement on collaboration and integrity as you proceed.

Logistics

You will complete this assignment individually.

Method of submission

Please submit your completed research article via email to Dr. Lyell (nllyell@mit.edu), with filename LastName_LabSection_Mod2.doc (for example, Lyell_TR_Mod2.doc).

Date of submission: April 18th

Your System engineering research article is due by 5 pm on Monday, April 18th.

Guidelines on formatting

Your main document (excluding figures) should be/have:

• .docx or .pdf
• 12-pt font
• 1-inch margins
• 1.5 or double spaced (excepting the abstract)

Figures can be created in a separate drawing program (such as powerpoint), and can either be embedded or submitted as a separate document.

Guidelines on Length

Not counting figures, report length should not exceed 13 pages. The following rough division is recommended:

• Introduction: 2-3 pages
• Methods: 3-4 pages
• Results: 4-5 pages
• Discussion: 2-3 pages

Concise writing is appreciated and rewarded! In other words, longer is not always better. You will not be penalized for going modestly over a section limit if you are being thorough yet concise. Conversely, you might technically stay within a section limit yet use more space than your content warrants, which would lower your evaluation.

Content Guidelines

Begin by reading the general guidelines for scientific writing. Carefully read the notes specific to Module 2 below:

Title and Abstract

The title and abstract do not count toward the page total and should both be on the first page of the final document. The introduction will start on the second page.

The title and abstract will be evaluated by Dr. Diana Chien and will account for 10% of the final grade for this assignment.

Introduction

Recall from the scientific writing guidelines the funnel structure for the introduction. Be sure to pay close attention to the feedback you've been given on your homework. Also, you may find that the BE Communication Lab is a terrific resource for providing suggestions on your Introduction. If the peer tutors in the BE Communication Lab, a scientifically literate audience, understand your motivation for the study -- you are in good shape!

The information you provide in your introduction should set up the investigative question in your introduction and should be supported by appropriate citations. Any and all information you found in another researcher's work should be cited. A failure to cite information you did not innately know is plagiarism.

• See below for more on citations in this assignment.

The introduction will be evaluated by Dr. Noreen Lyell and will account for 10% of the final grade for this assignment.

Methods

The methods section should include all of the procedures used in Module 2, though you should assume your audience is scientifically literate and somewhat familiar with common procedures (e.g. PCR). Remember that the methods should be divided into sub-sections that do not necessary correspond to the order in which experiments were completed in the laboratory.

Important things to consider:

• Do not use volumes, instead include final concentrations
• Include the manufacturer's information (name, location of headquarters) for all kits and reagents
• Be concise and clear in your description of the procedures

The methods section will be evaluated by Dr. Noreen Lyell and will account for 20% of the final grade for this assignment.

Results and Figures

Individual versus class-wide data

You should present just your individual results for all of the validation experiments. You may briefly comment on class-wide consistency if you wish. For the investigative flow cytometry experiment, you should include the class data. As with the Protein engineering summary, be sure that you are using the class data to construct a cohesive story...including all data with no real purpose will not be scored highly.

Suggested figures

The suggested list of figures below should be suitable for most of your write-ups (not necessarily in this order!), but you are welcome to make additions/deletions/modifications as you see fit. Be sure to present the data in whatever progression you feel tells the most logical story. Remember that the order of our experiments does not necessarily correspond to the best way to tell the story of this investigation.

• Schematics/diagrams
  • Overall approach (not every single method to get there!) and question being asked
  • Often the overview schematic is designed to support the first/overview paragraph of the Results section
• Figures
  • DNA-PK Western blot
  • NHEJ inhibitor dose response curve
  • Select raw flow cytometry images
    • Not all 12 of yours!
    • Ideally show how gating was determined, followed by one or two key representative experimental plots
• Figures and/or Tables
  • Class-wide flow cytometry results
  • Ultimately interested in NHEJ repair values for different conditions
    • Vertical bar plot with 95% confidence interval error bars is one good representation
  • Perform statistical comparisons where possible
    • We're fine with t-tests for 20.109 purposes, but you can use ANOVA or other multiple-comparison approaches if you wish
  • Some comment on interim results (e.g., typical mCherry to EGFP ratio and its consistency in intact case) is fine
  • Remember that some data may be excluded for clear and consistently applied reasons

The results will be evaluated by Dr. Leona Samson and will account for 50% of the final grade for this assignment.

Discussion

This section should realize all the good practices described in the Module 1 assignment in regards to concisely stating conclusions about your research, but do so at a more advanced level. You will be expected to cite the broader scientific literature more thoroughly than before, both to set up your investigative question in the introduction and to inform your analysis in the discussion. You should also propose specific future experiments and otherwise show that you deeply understand the meaning and significance of your results; for example, if you have a hypothesis about why a DNA topology had the relative repair frequency that it did, consider what follow-up experiments you might try. Also, make sure to do a bit of literature digging to determine if your results have any precedent or if your experiments are contrary to what has been reported. Modest speculation as to why that it the case is highly encouraged. The best scientific writers are creative in their discussion sections – convincing their readers that whatever the results, the study was interesting and contributes to forward movement of the field.

The discussion will be evaluated by Dr. Leona Samson and will account for 10% of the final grade for this assignment.

Citations

Follow the guidelines here for your reference section.

Evaluation

The full descriptive rubric for the research article can be found on the guidelines page.

The research article will be graded by Prof. Leona Samson, Dr. Diana Chien, and Dr. Noreen Lyell with input from Dr. Leslie McClain and Dr. Maxine Jonas.